UpSet: Make the UpSet plot

In zhongmicai/complexHeatmap: Make Complex Heatmaps

Description

Make the UpSet plot

Usage

UpSet(m,
    comb_col = "black",
    pt_size = unit(3, "mm"), lwd = 2,
    bg_col = "#F0F0F0", bg_pt_col = "#CCCCCC",
    set_order = order(set_size(m), decreasing = TRUE),
    comb_order = if(attr(m, "set_on_rows")) {
    order.comb_mat(m[set_order, ], decreasing = TRUE)
    } else {
    order.comb_mat(m[, set_order], decreasing = TRUE)
    },
    top_annotation = upset_top_annotation(m),
    right_annotation = upset_right_annotation(m),
    row_names_side = "left",
    ...)

Arguments

m	A combination matrix returned by make_comb_mat. The matrix can be transposed to switch the position of sets and combination sets.
comb_col	The color for the dots representing combination sets.
pt_size	The point size for the dots representing combination sets.
lwd	The line width for the combination sets.
bg_col	Color for the background rectangles.
bg_pt_col	Color for the dots representing the set is not selected.
set_order	The order of sets.
comb_order	The order of combination sets.
top_annotation	A HeatmapAnnotation object on top of the combination matrix.
right_annotation	A HeatmapAnnotation object on the right of the combination matrix.
row_names_side	The side of row names.
...	Other arguments passed to Heatmap.

Details

By default, the sets are on rows and combination sets are on columns. The positions of the two types of sets can be switched by transposing the matrix.

When sets are on rows, the default top annotation is the barplot showing the size of each combination sets and the default right annotation is the barplot showing the size of the sets. The annotations are simply constructed by HeatmapAnnotation and anno_barplot with some parameters pre-set. Users can check the source code of upset_top_annotation and upset_right_annotation to find out how the annotations are defined.

To change or to add annotations, users just need to define a new HeatmapAnnotation object. E.g. if we want to change the side of the axis and name on top annotation:

    Upset(..., top_annotation = 
        HeatmapAnnotation(
           "Intersection size" = anno_barplot(
               comb_size(m), 
               border = FALSE, 
               gp = gpar(fill = "black"), 
               height = unit(2, "cm"),
               axis_param = list(side = "right")
           ), 
           annotation_name_side = "right", 
           annotation_name_rot = 0)
    )  

To add more annotations on top, users just add it in HeatmapAnnotation:

    Upset(..., top_annotation = 
        HeatmapAnnotation(
           "Intersection size" = anno_barplot(
               comb_size(m), 
               border = FALSE, 
               gp = gpar(fill = "black"), 
               height = unit(2, "cm"),
               axis_param = list(side = "right")
           ), 
           "anno1" = anno_points(...),
           "anno2" = some_vector, 
           annotation_name_side = "right", 
           annotation_name_rot = 0)
    )  

And so is for the right annotations.

UpSet returns a Heatmap-class object, which means, you can add it with other heatmaps and annotations by + or %v%.

Examples

set.seed(123)
lt = list(a = sample(letters, 10),
          b = sample(letters, 15),
          c = sample(letters, 20))
m = make_comb_mat(lt)
UpSet(m)
UpSet(t(m))

m = make_comb_mat(lt, mode = "union")
UpSet(m)
UpSet(m, comb_col = c(rep(2, 3), rep(3, 3), 1))

# compare two UpSet plots
set.seed(123)
lt1 = list(a = sample(letters, 10),
          b = sample(letters, 15),
          c = sample(letters, 20))
m1 = make_comb_mat(lt1)
set.seed(456)
lt2 = list(a = sample(letters, 10),
          b = sample(letters, 15),
          c = sample(letters, 20))
m2 = make_comb_mat(lt2)

max1 = max(c(set_size(m1), set_size(m2)))
max2 = max(c(comb_size(m1), comb_size(m2)))

UpSet(m1, top_annotation = upset_top_annotation(m1, ylim = c(0, max2)),
    right_annotation = upset_right_annotation(m1, ylim = c(0, max1)),
    column_title = "UpSet1") +
UpSet(m2, top_annotation = upset_top_annotation(m2, ylim = c(0, max2)),
    right_annotation = upset_right_annotation(m2, ylim = c(0, max1)),
    column_title = "UpSet2")

zhongmicai/complexHeatmap documentation built on May 7, 2019, 6:11 a.m.